[ensembl-dev] Gene Annotated on PAR-1 region of Y Chromosome

[Susan Fairley]

Hi,

Bio X2Y wrote:
> Hi,
> 
> I'm hoping someone might be able to explain why Ensembl 59 has an 
> annotated gene in the PAR-1 region of Y (gene_id 98559)? From what I 
> understand, it only makes sense to define genes on the PAR-1 region of X?

This gene extends beyond the PAR region, into sequence that is unique to 
the Y chromosome. The annotation comes from the manual annotation 
provided by the HAVANA group, which is merged with the Ensembl human 
gene set. As you will see, the end of the gene (2722682) lies beyond the 
end of the PAR region (2649520).

homo_sapiens_core_59_37d >select * from gene where seq_region_id =27507 
and seq_region_start between 10000 and 2649521;
+---------+----------------------+-------------+---------------+------------------+----------------+-------------------+-----------------+--------+--------+----------------------------------------------------------+------------+-------------------------+----------------------+
| gene_id | biotype              | analysis_id | seq_region_id | 
seq_region_start | seq_region_end | seq_region_strand | display_xref_id 
| source | status | description 
      | is_current | canonical_transcript_id | canonical_annotation |
+---------+----------------------+-------------+---------------+------------------+----------------+-------------------+-----------------+--------+--------+----------------------------------------------------------+------------+-------------------------+----------------------+
|   98559 | processed_transcript |        8049 |         27507 | 
   2620124 |        2722682 |                 1 |         6436017 | 
havana | KNOWN  | Xg pseudogene, Y-linked 2 [Source:HGNC 
Symbol;Acc:34022] |          1 |                  253763 | NULL 
         |
+---------+----------------------+-------------+---------------+------------------+----------------+-------------------+-----------------+--------+--------+----------------------------------------------------------+------------+-------------------------+----------------------+
1 row in set (0.00 sec)


> 
> A second question, partially related - how does Ensembl define the 
> coordinates PAR regions? Is some comparison tool run to estimate the 
> regions of similarity, or are the coordinates provided as part of 
> GRCh37? I'm not aware of these being mentioned in GRCh37, other than a 
> note for the "lite" version of the assembly.

We take the coordinates provided by the GRC. This page,
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/index.shtml,
provides an overview of the assembly exceptions, including the PAR 
regions and their coordinates.

I hope this is of help.

Regards,
Susan.

> 
> 
> Thanks for your help.
> 
> 
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